6B1O

The structure of DPP4 in complex with Vildagliptin Analog

• PDB DOI: https://doi.org/10.2210/pdb6B1O/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-09-18 Released: 2017-09-27 
• Deposition Author(s): Scapin, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.202 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

A comparative study of the binding properties, dipeptidyl peptidase-4 (DPP-4) inhibitory activity and glucose-lowering efficacy of the DPP-4 inhibitors alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin in mice.

Berger, J.P., SinhaRoy, R., Pocai, A., Kelly, T.M., Scapin, G., Gao, Y.D., Pryor, K.A.D., Wu, J.K., Eiermann, G.J., Xu, S.S., Zhang, X., Tatosian, D.A., Weber, A.E., Thornberry, N.A., Carr, R.D.

(2018) Endocrinol Diabetes Metab 1: e00002-e00002

• PubMed: 30815539 
• DOI: https://doi.org/10.1002/edm2.2
• Primary Citation of Related Structures:  
  6B1E, 6B1O


• PubMed Abstract: 
  

  Since 2006, DPP-4 inhibitors have become established therapy for the treatment of type 2 diabetes. Despite sharing a common mechanism of action, considerable chemical diversity exists amongst members of the DPP-4 inhibitor class, raising the question as to whether structural differences may result in differentiated enzyme inhibition and antihyperglycaemic activity.

---

Organizational Affiliation: 

Merck& Co., Inc. Kenilworth NJ USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 174.11 kDa 
• Atom Count: 13,880 
• Modelled Residue Count: 1,456 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	728	Homo sapiens	Mutation(s): 1  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487 GTEx:  ENSG00000197635

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G, H, I, J, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8S (Subject of Investigation/LOI)	N [auth A], P [auth B]	(2S)-2-amino-1-[(1S,3S,5S)-3-(aminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(1r,3R,5S,7S)-3,5-dihydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-one C18 H29 N3 O3 NFCLGRKAEZJOPE-KAARGAEXSA-N
NAG	L [auth A], M [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.202 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.515	α = 90
b = 123.342	β = 90
c = 130.958	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Scapin, G.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2019-03-13
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary